I've seen several mods that are not "kronometerized".  Those mods are likely hardcoded to a 6 (or 24) hour day.  From what I've been told, there are internal variables that define the length of day and year, and unless a mod references those variables, it's not going to work correctly with Kronometer.  It's my understanding that it's the other mods that must change to make it work.  Until that happens (if it ever does), you'll just have to deal with the inconvenience.